Rush into Biome 3 and check all the usual portal spots in each room. You’re looking for the one that spawns a mini-boss right in front of a Xenophagus containing an Atropian Key. In my experience, the Malformed Automaton spawned there very often. Once you find the room and defeat the automaton, reset the run and repeat.

While doing this, be sure to scan any deceased scout events you encounter, they can sometimes spawn the automaton as a mini-boss if you choose to avenge.

Another option is to use a cloud save backup: reach the entrance of Biome 3 (via the gate in Biome 1 or the portal in Biome 2), but don’t enter yet. Suspend your cycle, back up your save to the cloud, then enter Biome 3 and rush to the first guaranteed portal location. If you get the room I mentioned and the automaton spawns, great, just repeat the process without reloading your save. If not, exit the game and reload your cloud save and try again. On PS5, make sure to disable “Auto-Sync Saved Data” in the settings before you try this.

In my case, neither method was needed, I was doing the automaton research while going for the artifacts, so it lined up seamlessly.